Uptake of homologous single-stranded fragments by superhelical DNA. IV. Branch migration.

Abstract The uptake of a homologous single-stranded fragment by superhelical DNA produces a complex that contains a stable displacement loop. When the circular DNA was relaxed by the random action of pancreatic DNAase, complexes dissociated by a process which requires that the single-stranded arm of the D-loop be intact. We attribute the dissociation to branch migration, the exchange of like strands at a branch point. The kinetics of dissociation were biphasic. A fraction of the nicked complexes dissociated in a few seconds, the rest dissociated much more slowly. The fraction of molecules that dissociated slowly was directly related to the length of the third strand, and inversely related to temperature. Salt also inhibited dissociation. Under physiological conditions, 37 °C and 0.15 m -NaCl, more than half of complexes containing a third strand of 1000-nucleotide residues survived for at least one minute. These observations provide a guide to handling certain natural or synthetic branched derivatives of DNA. Analyzing our data by the method of Thompson et al. (1976), we have estimated that the time for the exchange of one nucleotide for another at a single-stranded branch is 12 microseconds; but the calculated value depends strongly upon the assumption that single-strand branch migration occurs by a random walk.